Ortoleva, Peter - Indiana University - Department of Chemistry

研究领域

Physical Chemistry/Chemical Biology

近期论文

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Y. V. Sereda, P. J. Ortoleva. A multiscale variational approach to the kinetics of viscous classical liquids: The coarse-grained mean field approximation. The Journal of CHemical Physics (2014). 140(134104). doi: 10.1063/1.4869860. A. Abi Mansour, P. J. Ortoleva. Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision. Journal of Chemical Theory and Computation, (2014). A. Singharoy, A. Polavarapu, H. Joshi, M. Baik, and P. Ortoleva. Epitope Fluctuation in the Human Papillomavirus Are Under Dynamic Allosteric Control:A Computational Evaluation of a New Vaccine Design Strategy. Journal of the American Chemical Society. 2013. 135(40) 18458-18468. doi: 10.1021/ja407489r H. Joshi, K. Lewis, A. Singharoy, P. Ortoleva. Epitope Engineering and Molecular Metrics of Immunogenicity: A Computational Approach to VLP-based Vaccine Design. Vaccine. 31(42): 4841-4847. http://www.sciencedirect.com/science/article/pii/S0264410X13010669 R. Quick, A. Singharoy, P. Ortoleva, Quasiperiodic Oscillation and Possible Second Law Violation in a Nanosystem, Chemical Physics Letters, 571 (2013), 61-65. http://www.sciencedirect.com/science/article/pii/S0009261413004466 A. Singharoy, H. Joshi, P. Ortoleva. Multiscale Macromolecular Simulation: Role of Evolving Ensembles. Journal of Chemical Information and Modeling. 2012. 52(10) 2638-49. doi: 10.1021/ci3002952 Abhishek Singharoy, Yuriy Sereda, and Peter J. Ortoleva, "Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters", J. of Chemical Theory and Computation 8 (2012) #4, 1379-1392. PMCID: PMC3361912. doi:10.1021/ct200574x Yuriy V. Sereda, Peter J. Ortoleva, "Variational methods for time-dependent classical many-particle systems", Physica A 392 (2013) #4, 628-638. Pankavich, S. and Ortoleva, P, Nanosystem Self-Assembly Pathways Discovered via All-Atom Multiscale Analysis. Journal of Physical Chemistry. (2012) 116 (29), (2012) p. 8355-8362. doi:10.1021/jp210407e. Sereda, Y., Singharoy, A., Jarrold, M., and Ortoleva, P., Discovering Free Energy Basins for Macromolecular Systems via Guided Multiscale Simulation. Journal of Physical Chemistry, (2012). vol. 116 (29). p. 8534-44. Singharoy, A., Joshi, H., Ortoleva, P. and Miao, Y., Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of BionanoSystems. Journal of Physical Chemistry B , vol. 116 (29), (2012) p. 8423-34. doi:10.1021/jp2119247 Joshi H, S. Cheluvaraja, E. Somogyi, DR Brown, P Ortoleva, A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: A possible indicator of immunogenicity. Vaccine. 2011 Nov 28;29(51):9423-30. doi:10.1016/j.vaccine.2011.10.039 Joshi, H., Singharoy, A., Sereda, Y., Cheluvaraja, S., and P. Ortoleva, Multiscale simulation of microbe structure and dynamics (2011). Prog. Biophys Mol. Biol. 107: 200-217. doi:10.1016/j.pbiomolbio.2011.07.006 Fontus, M. and P. Ortoleva, Electrometabolomic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis. Journal of Biotech Research, 2011. 3:37-50. Shreif, Z. and P. Ortoleva, Scaling Behavior of Quantum Nanosystems: Emergence of Quasi-particles, Collective Modes, and Mixed Exchange Symmetry States. Journal of Chemical Physics, 2011. 134, 104106 (2011). doi:10.10631/1.3560450 (11 pages). Shreif, Z. and P. Ortoleva, Multiscale Born-Oppenheimer Theory of Collective Electron-Nuclear Dynamics in Nanosystems. Journal of Theoretical and Computational Chemistry, 2011. 10 (5), 605-614; doi: 10.1142/S0219633611006669. Singharoy, A., et al., eds. Simulating Microbial Systems: Addressing Model uncertainty/incompleteness via Multiscaling and Entropy methods Microbial Systems Biology: Methods and Protocols, ed. A. Navid. 2010, Springer Science: New York. Fontus, F. and P. Ortoleva, Electrophysiological-Metabolic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis. Microbial Systems Biology: Methods and Protocols, ed. A. Navid. 2010, Springer Science: New York. Singharoy, A., S. Cheluvaraja, and P. Ortoleva, Order Parameters for Macromolecules: Application to Multiscale simulations. J. Chem. Phys, 2011. 134, 044104; doi: 10.1063/1.3524532. Miao, Y., and P. Ortoleva, Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation. Biopolymers, 2010. 93(1): p.61-73.